Sodium in PDB 6rij: CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436
Enzymatic activity of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436
All present enzymatic activity of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436:
2.7.11.22;
Protein crystallography data
The structure of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436, PDB code: 6rij
was solved by
J.Skerlova,
P.Rezacova,
J.Brynda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
162.95 /
2.20
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.310,
148.060,
162.960,
90.00,
90.51,
90.00
|
R / Rfree (%)
|
20.4 /
23.8
|
Sodium Binding Sites:
The binding sites of Sodium atom in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436
(pdb code 6rij). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436, PDB code: 6rij:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6rij
Go back to
Sodium Binding Sites List in 6rij
Sodium binding site 1 out
of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:38.5
occ:1.00
|
O
|
A:HOH413
|
3.1
|
40.0
|
1.0
|
O
|
A:HOH416
|
3.2
|
38.6
|
1.0
|
N
|
A:TYR269
|
3.5
|
34.9
|
1.0
|
CG2
|
A:VAL226
|
3.7
|
79.8
|
1.0
|
CD2
|
A:HIS268
|
3.8
|
50.2
|
1.0
|
CD2
|
A:TYR269
|
3.9
|
38.1
|
1.0
|
NE2
|
A:HIS268
|
3.9
|
49.8
|
1.0
|
CG
|
A:HIS268
|
3.9
|
46.5
|
1.0
|
CA
|
A:HIS268
|
4.0
|
35.9
|
1.0
|
CB
|
A:TYR269
|
4.0
|
38.5
|
1.0
|
CE1
|
A:HIS268
|
4.0
|
53.5
|
1.0
|
ND1
|
A:HIS268
|
4.1
|
52.7
|
1.0
|
C
|
A:HIS268
|
4.2
|
34.0
|
1.0
|
NH1
|
A:ARG245
|
4.4
|
43.5
|
1.0
|
CA
|
A:TYR269
|
4.4
|
35.7
|
1.0
|
CG
|
A:TYR269
|
4.4
|
38.5
|
1.0
|
CG1
|
A:VAL226
|
4.5
|
63.3
|
1.0
|
CB
|
A:HIS268
|
4.6
|
42.8
|
1.0
|
CB
|
A:VAL226
|
4.8
|
64.7
|
1.0
|
CE2
|
A:TYR269
|
4.9
|
37.2
|
1.0
|
O
|
A:LEU267
|
5.0
|
33.3
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6rij
Go back to
Sodium Binding Sites List in 6rij
Sodium binding site 2 out
of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:50.2
occ:1.00
|
O
|
B:GLN203
|
2.5
|
51.4
|
1.0
|
O
|
B:MET200
|
2.6
|
54.4
|
1.0
|
O
|
B:ILE206
|
2.7
|
44.8
|
1.0
|
C
|
B:GLN203
|
3.7
|
51.1
|
1.0
|
C
|
B:MET200
|
3.7
|
57.5
|
1.0
|
C
|
B:ILE206
|
3.8
|
45.0
|
1.0
|
CB
|
B:GLN203
|
4.3
|
54.7
|
1.0
|
O
|
B:LYS201
|
4.3
|
61.2
|
1.0
|
CA
|
B:GLN203
|
4.3
|
54.0
|
1.0
|
CG
|
B:MET200
|
4.4
|
55.9
|
1.0
|
N
|
B:GLN203
|
4.4
|
52.9
|
1.0
|
N
|
B:LYS201
|
4.5
|
58.8
|
1.0
|
CA
|
B:THR207
|
4.5
|
48.4
|
1.0
|
C
|
B:LYS201
|
4.5
|
61.4
|
1.0
|
CG2
|
B:THR207
|
4.6
|
49.2
|
1.0
|
CA
|
B:LYS201
|
4.6
|
64.2
|
1.0
|
N
|
B:ILE206
|
4.6
|
47.6
|
1.0
|
N
|
B:THR207
|
4.6
|
47.7
|
1.0
|
CA
|
B:MET200
|
4.7
|
54.2
|
1.0
|
N
|
B:PRO204
|
4.8
|
52.2
|
1.0
|
C
|
B:PRO204
|
4.8
|
57.8
|
1.0
|
CA
|
B:ILE206
|
4.8
|
46.9
|
1.0
|
O
|
B:PRO204
|
4.9
|
61.3
|
1.0
|
SD
|
B:MET200
|
4.9
|
58.3
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6rij
Go back to
Sodium Binding Sites List in 6rij
Sodium binding site 3 out
of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na302
b:39.2
occ:1.00
|
O
|
C:HOH420
|
3.0
|
37.1
|
1.0
|
O
|
C:HOH408
|
3.3
|
35.4
|
1.0
|
N
|
C:TYR269
|
3.4
|
34.4
|
1.0
|
CD2
|
C:HIS268
|
3.7
|
51.0
|
1.0
|
NE2
|
C:HIS268
|
3.8
|
54.8
|
1.0
|
CG2
|
C:VAL226
|
3.9
|
79.6
|
1.0
|
CD2
|
C:TYR269
|
3.9
|
35.1
|
1.0
|
CG
|
C:HIS268
|
3.9
|
48.4
|
1.0
|
CA
|
C:HIS268
|
4.0
|
37.7
|
1.0
|
CE1
|
C:HIS268
|
4.1
|
55.5
|
1.0
|
CB
|
C:TYR269
|
4.1
|
34.7
|
1.0
|
ND1
|
C:HIS268
|
4.1
|
53.5
|
1.0
|
C
|
C:HIS268
|
4.2
|
36.6
|
1.0
|
CA
|
C:TYR269
|
4.4
|
34.8
|
1.0
|
CG
|
C:TYR269
|
4.4
|
35.3
|
1.0
|
NH1
|
C:ARG245
|
4.5
|
43.1
|
1.0
|
CB
|
C:HIS268
|
4.6
|
41.8
|
1.0
|
CG1
|
C:VAL226
|
4.7
|
67.1
|
1.0
|
O
|
C:LEU267
|
4.9
|
35.4
|
1.0
|
CE2
|
C:TYR269
|
4.9
|
32.6
|
1.0
|
CB
|
C:VAL226
|
4.9
|
69.0
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6rij
Go back to
Sodium Binding Sites List in 6rij
Sodium binding site 4 out
of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na501
b:46.4
occ:1.00
|
O
|
D:GLN203
|
2.6
|
50.3
|
1.0
|
O
|
D:MET200
|
2.6
|
60.2
|
1.0
|
O
|
D:ILE206
|
2.7
|
42.4
|
1.0
|
C
|
D:MET200
|
3.7
|
58.9
|
1.0
|
C
|
D:GLN203
|
3.8
|
52.9
|
1.0
|
C
|
D:ILE206
|
3.9
|
45.1
|
1.0
|
O
|
D:LYS201
|
4.3
|
59.4
|
1.0
|
CB
|
D:GLN203
|
4.3
|
54.9
|
1.0
|
CG
|
D:MET200
|
4.4
|
53.1
|
1.0
|
CA
|
D:GLN203
|
4.4
|
52.7
|
1.0
|
CG2
|
D:THR207
|
4.4
|
47.8
|
1.0
|
N
|
D:GLN203
|
4.4
|
54.4
|
1.0
|
N
|
D:LYS201
|
4.4
|
65.4
|
1.0
|
C
|
D:LYS201
|
4.5
|
65.0
|
1.0
|
CA
|
D:LYS201
|
4.5
|
69.3
|
1.0
|
CA
|
D:THR207
|
4.5
|
46.3
|
1.0
|
O
|
D:HOH637
|
4.5
|
43.5
|
1.0
|
N
|
D:THR207
|
4.7
|
44.3
|
1.0
|
O
|
D:PRO204
|
4.7
|
57.6
|
1.0
|
CA
|
D:MET200
|
4.7
|
55.4
|
1.0
|
N
|
D:ILE206
|
4.7
|
45.5
|
1.0
|
C
|
D:PRO204
|
4.8
|
55.3
|
1.0
|
N
|
D:PRO204
|
4.8
|
49.6
|
1.0
|
SD
|
D:MET200
|
4.9
|
54.9
|
1.0
|
CB
|
D:MET200
|
5.0
|
52.1
|
1.0
|
CA
|
D:ILE206
|
5.0
|
47.5
|
1.0
|
|
Reference:
J.Skerlova,
P.Rezacova,
J.Brynda.
CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 To Be Published.
Page generated: Tue Oct 8 13:12:26 2024
|